Polypeptides antiparallel pleated-sheet structure

Figure II-2 Major elements of secondary structure of proteins. Left, the a-helix right, representation of the antiparallel pleated sheet structures for polypeptides. (After Pauling, L., and R. B. Corey (1951). Proc Natl Acad Sci USA 37 729).

Fig. 6. The antiparallel pleated sheet structure of polypeptide chains. (Marsh et al, 1955.)...

Fig. 10.4. Representation of (a) the parallel and (b) the antiparallel pleated-sheet structures for polypeptides (Pauling and Corey, 1951). (From Mahler and Cordes, 1966.)...

Carbonic Anhydrase.—Strandberg and his colleages" have calculated a 2 A resolution electron-density map of human erythrocyte carbonic anhydrase C. A polypeptide chain of 258 amino-acid residues is indicated, and two sequenced fragments have been fitted in positions 1—88 and 224— 258. The structure has a gross shape of 41 x 41 x 47 A and is built essentially of three layers. Seven distorted sections of right-handed a-helix are in the surface layers. In contrast the middle layer is an extensive mainly antiparallel pleated sheet structure with a total twist of 220° and comprising 37% of the total residues. There are aromatic regions between the central sheet and the surface layers. 

In the calculations of the electronic structure of these polypeptides, we applied the all-valence electron MINDO crystal-orbital method in its MINDO/3 parametrization. The calculations involved atomic coordinates corresponding to the antiparallel-) -pleated-sheet structure of Pauling and Corey S hence we had a combined symmetry operation in the case of poly( y) each gly unit was obtained in this polymer from its neighboring one by a translation along the helical axis through 3.25 A and by a simultaneous 180° rotation around it. In order to preserve the cyclic property of the Fock hypermatrix of the whole polymer (which is... 

The p-pleated sheet structure occurs in fibrous as well as globular proteins and is formed by intermolecular hydrogen bonds between a carboxyl group oxygen of one amino acid and an amine hydrogen of an adjacent polypeptide chain. Parallel p-pleated sheets form when the adjacent polypeptide chains are oriented in one direction (from N-terminal to C-terminal end or vice versa). Antiparallel p-pleated... 

Figure 3-1. a. Alpha-helix structure for a polypeptide or protein b. Pleated sheet structures, depicting parallel (1) and antiparallel (2) variants (Elias 1997, reprinted courtesy ofWiley-VCH.). 

Pleated sheet structures are parallel or antiparallel. In the local minimum in the Ramachandran qt/y/ plot (Fig. 19.3) of y3-pleated sheet structures, two configurations are possible, with parallel and antiparallel orientation of the polypeptide strands (Fig. 19.6). The strands are linked by mferchain N-H 0=C hydrogen bonds, which run both ways between the strands and produce a characteristically different pattern in parallel and antiparallel sheets. It is a particular stereochemical feature of the /7-pleated sheets that amino acid side-chains point alternately up and down, and adjacent side-chains interact sterically to produce a right-handed twist [597, 5981 (see Fig. 19.7 a). The regular pattern of a /7-sheet can be interrupted locally by insertion of an extra amino acid, giving rise to a so-called /7-bulge [599]. 

The (3-strand sequences are stretched out conformations of these polypeptide sections and are typically stabilized by inter-strand hydrogen bonds between keto (C = 0) oxygens and peptide bond NHs, the strands being arrayed in an antiparallel fashion. This type of secondary structure is favoured by amino acid residues with small R groups (such as Gly, Ala and Ser) that minimize steric overlap between chains. Thus a well-known protein having this type of secondary structure is silk fibroin that has a high proportion of repeated sequences involving Gly, Ala and Ser and an extensive antiparallel (3-pleated sheet structure. The macroscopic properties of silk fibroin (flexibility but lack of stretchability) reflect this type of secondary structure at the molecular level. 

There are two ways in which proteins chains can form the pleated sheet structure. One is with the chains running in the same direction i.e. the -COOH or NH2 ends of the polypeptide chains lying all at the top or all at the bottom of the sheet. This is called parallel pleated-sheet structure. In another type, known as antiparallel p-pleated sheet structure, the polypeptide chains alternate in such a way that the -COOH end of the one polypeptide is next to the -NH2 end of the other i.e., polypeptide chains run in opposite directions. 

Repeating sequences of amino acids with small, compact R-groups (e.g., glycine, alanine) tend to form the (3, or pleated sheet, structure, which consists of parallel (Fig. 2-3a) or antiparallel (Fig. 2-36) polypeptide chains linked by interchain hydrogen bonds. Silk is an example of the antiparallel sheet. 

The classical polypeptide conformations are the a-helix and the parallel and antiparallel -pleated sheets due to Pauling and colleagues [46,47]. These conformations can occur separately in fibrous proteins or they can often be beautifully combined, as in certain globular proteins such as triose phosphate isomerase [48] and carboxypeptidase A [49]. The interesting motifs constituting the anatomy of some globular proteins have been emphasized by the work of Richardson [50], and a combination of pleated sheet and a-helix was early proposed as a structural motif for dynamic voltage dependent channel formation [51,52]. Our concern here, however, is to characterize separately these conformations in order that a view of more complex combinations of these structures can be correctly obtained. 

Hydrogen bonds stabilize secondary structures. These can be within a chain (as in an ot-helix) or between different chains (as in a / -pleated sheet). Figure 6.6 illustrates how hydrogen bonds stabilize four different helical structures. When hydrogen bonds stabilize adjacent polypeptide chains in / -sheet structures, the adjacent chains can be oriented parallel or antiparallel to each other. When both chains are parallel, they have the same amino to carboxyl orientation. When they are antiparallel, the two chains have opposite amino to carboxyl orientations. 

These represent the sheetlike arrangement of the polypeptide chains. The hydrogen bonds are found between the adjacent polypeptide chains. The polypeptide chains involved in the pleated sheet structure can be either parallel or antiparallel. Hydrogen bonds stabilize the p-pleated sheet (see Figure 28-7). 

About a year ago, in the course of the consideration of configurations of polypeptide chains with favored orientations around single bonds, we described two pleated-sheet structures. These structures are suited to polypeptide chains constructed entirely of l amino-acid residues or of d amino-acid residues. In one pleated sheet alternate polypeptide chains are antiparallel, and in the other they are parallel. The amide groups have the trans configuration. 

In contrast to the a-helical structure of the a-K. discussed above, the -K. have -pleated sheet structure. The most prominent representative of this class is silk fibroin (iff, 365,000, 2 subunits). Here the chains run antiparallel rather than parallel, and form a zig-zag structure. The formation of hydrogen bonds between the -CH(=0) and -NH- groups of neighboring chains stabilizes the pleated sheet structure. Together with weak hydrophobic interactions, the hydrogen bonds link pairs of polypeptides into a three-dimensional protein complex. These are additionally stabilized, in silk, by a water-soluble protein, sericin. The resultant fiber is very resistant and flexible, but only slightly elastic. The amino acid sequence which repeats over long stretches of the chain is, for silk fibroin, (Gly-Ser-Gly-Ala-Gly-Ala-) . 

F g.8.p-Pleated sheet structure antiparallel arrangement of two polypeptide chains. 

Collagen (see) has a specialized structure containing interchain, hydrogen-bonded, left-handed helices. Otherwise, all known P. helices are right-handed, but the possibility remains that left-handed helices might be found in P. which have not yet been analysed by X-ray diffraction, e.g. membrane P. In the pleated sheet structure, the polypeptide chain is more or less stretched out, and neighboring lengths of chain can be parallel or antiparallel (with respect to their N- and C-termini), e.g. the pleated sheet structure of silk fibroin (Fig. 8) consists of antiparallel polypeptide chains. 

Figure 16.22 Hydrogen bonds (a) in a parallel S-pleated sheet structure, in which all the polypeptide chains are oriented in the same direction, and (b) in an antiparallel /S-pleated sheet, in which adjacent polypeptide chains run in opposite directions. For color key, see Figure 16.19.

Poly(L-tyrosine), which adopts the antiparallel pleated sheet conformation in water at low ionization, has also been studied by far ultraviolet c.d. It was suggested that lower molecular weight polymers possessed only a few polypeptide chains folded into long open-chain / -structures, whereas a higher molecular weight polymer took up a more compact shape, in which the /S-sheet had folded over on to itself into a double-layer. This could be regarded as the first prototype of tertiary structure observed in a -forming homopolymer. 

The level of detailed knowledge is much higher for certain repressor proteins and their interactions with DNA. The structures of four polypeptides that specifically bind to DNA have been determined recently, namely the lac repressor protein,< - > the cro repressor protein from bacteriophage, the catabolite gene activator protein from Escheria coli, and the amino-terminal fragment of the Cl repressor protein from bacteriophage In addition to the primary structure of the polypeptide, the sequence of the base pairs in that DNA fragment to which the relatively short polypeptide is bound, is known. Furthermore, structural data about the conformation of the peptide backbone are available, e.g., strands of a-helices followed by antiparallel -pleated sheets. 

L-aspartate (7), y-[2-(9-carbazoIyl)ethyl]-L-glutamate(8), N -[(9-carbazolyl)-carbonyl]-L-lysine (9), and 2-[(9-carbazolyI)ethyl]-L-cysteine (10). No detailed information on the optical rotatory properties of the indicated polymers has been reported, whereas a great deal of attention has been focused on the dichroic absorption properties especially for different samples of poly(8). While the first three polymers are characterized by an a-helix structure in both solution and solid state, poly(lO) may assume antiparallel pleated-sheet and normal antiparallel P-forms. Apparently, the presence of the bulky side group does not substantially affect the conformational structure imposed by the polypeptide backbone. Additionally in concentrated solutions, the cholesterogenic propensity of polypeptides such as those based on L-glutamic acid, L-aspartic acid, and L-lysine is not appreciably influenced by the steric and electronic characteristics of the carbazole moiety anchored via different spacers to the peptide units. 

FIGURE 4-7 The /8 conformation of polypeptide chains. These top and side views reveal the R groups extending out from the /3 sheet and emphasize the pleated shape described by the planes of the peptide bonds. (An alternative name for this structure is /3-pleated sheet.) Hydrogen-bond cross-links between adjacent chains are also shown, (a) Antiparallel /3 sheet, in which the amino-terminal to carboxyl-terminal orientation of adjacent chains (arrows) is inverse, (b) Parallel f) sheet. 

Antiparallel /3-pleated sheet (/3 sheet). A hydrogen-bonded secondary structure formed between two or more extended polypeptide chains. 

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